Conformation and trapping rate of DNA at a convergent stagnation point

Abstract

We use a lattice-Boltzmann based Brownian dynamics simulation to investigate the elongation of DNA at a convergent stagnation point trapped by a uniform attractive potential. The trapping rate of the DNA is not sensitive to the potential and, consistent with a mean field theory, scales as the Peclet number, Pe(1/3) . Surprisingly, we find that the coiled state is favored over the stretched state at high Pe. The final elongation is determined by conformation changes during transport to the stagnation point, rather than hydrodynamic stretching at that point.